STS manifest editor deletes all error and warning markers on document save. This is a problem with the YEdit editor that STS manifest editor extends, and not with vscode manifest language server. This is just a temporary workaround until STS no longer needs the YEdit-based editor and uses LSP4E editor instead.
headless services
The main parts of the tooling for Spring Boot apps are implemented as headless services, running in separate processes. Those services can be consumed in existing IDEs by using the Language Server Protocol from Visual Studio Code.